For whatever reason my PI decided to submit many long amplicons for PacBio sequencing without barcoding each amplicon. He now wants to know how much variation exists between the samples. I was looking at the Long Amplicon Analysis (LAA) tool and it says it can generate consensus based on unique individual molecules. I don't know if it can account for each molecule without barcoding.

Is there a way to call variation on this mixed sample file? I already did a simple bam-readcount and it gives too many possible variants at each site. I figured I need a true variant caller to distinguish true variants. Samtools/Bcftools mpileup basically stalls out with nothing written to file. I am assuming it can't handle the long reads.